What images do you use?
Where have the clipping paths been created?
How do you copy the file? Do you package? That is the best method to copy a whole file with all assets to another folder.
I guess we receive them as a package (I'm not the original receiver of the files).
When I copy to another folder - I just copy/paste
A Jpeg can have no clipping path, or 1 or more. If you have paths in Photoshop, you can designate one as the default path. Once placed in InDesign, it will use the one designated in Photoshop, but you can change it in InDesign. If you click on the image and go to Object>Clipping Path>Options. That will bring up a window where you can select from the paths that were saved in the Jpeg, or have InDesign create one (although it will usually be not as good as if it were done in Photoshop, so only use that as a last resort). You can also select None as the path for a Jpeg that has one or more, and it will act as if it had none.
What you should check is whether these particular Jpegs were saved in Photoshop without designating a path as default, and possibly it was turned on after it was placed. If that were the case, it could be that the setting for the clipping path was changed to the default, which is to use what is in the Jpeg, and not the changes to the path after it was placed. I'm not sure how this could be switched off by copying, but it's what I would probably check first.
Of course, a JPG can have a clipping path but no alpha channel.